MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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Network Comparison Type	Rank	Gene	Hugo	description	Value Type	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 1951 to 2000 of 2060 in total

Network Comparison Type  : Subtracted
Interaction Map  : Low confidence
Filtered  : 1
red  : 0
network_comparison  : 0
green  : 0

Rank	Hugo	description	Value Type
5034	RAP1GDS1	rap1 gtpase-gdp dissociation stimulator 1 (smg p21 stimulatory gdp/gtp exchange protein) (smg gds protein) (exchange factor smggds). [swissprot;acc:p52306]	Squared
			Rooted
	SLCO5A1	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	Ranked
5035	LPIN1	lipin 1. [swissprot;acc:q14693]
	SLCO5A1	solute carrier family 21 member 15 (organic anion transporter polypeptide-related protein 4) (oatp-rp4) (oatprp4). [swissprot;acc:q9h2y9]	Measured
			Squared
			Rooted
5036	LPIN1	lipin 1. [swissprot;acc:q14693]	Measured
			Squared
			Rooted
	LPIN3	lipin 3 (lipin 3-like) (fragments). [swissprot;acc:q9bqk8]	Ranked
5037			Measured
			Squared
			Rooted
	PXDN	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	Ranked
5038	LRRC6	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]
	PXDN	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	Measured
			Squared
			Rooted
5039	CENPB	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	Ranked
	LRRC6	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	Measured
			Squared
			Rooted
5040	CENPB	major centromere autoantigen b (centromere protein b) (cenp-b). [swissprot;acc:p07199]	Measured
			Squared
			Rooted
	LRRFIP1	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Ranked
5041			Measured
			Squared
			Rooted
	NAGK	n-acetylglucosamine kinase (ec 2.7.1.59) (glcnac kinase). [swissprot;acc:q9uj70]	Ranked
5042			Measured
			Squared
			Rooted
	TTR	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	Ranked
5043	no value	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]
	TTR	transthyretin precursor (prealbumin) (tbpa) (ttr) (attr). [swissprot;acc:p02766]	Measured
			Squared
			Rooted
5044	no value	late endosomal/lysosomal mp1 interacting protein (p14) (hspc003). [swissprot;acc:q9y2q5]	Measured
			Squared
			Rooted
	CD207	langerhans cell specific c-type lectin. [refseq;acc:nm_015717]	Ranked
5045			Measured
			Squared
			Rooted
	CYB561D2	putative tumor suppressor 101f6. [refseq;acc:nm_007022]	Ranked
5046			Measured
			Squared
			Rooted

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.